According to Nikkei newspaper, Amazon Japan is planning to provide mobile data service as an MVNO. It has been rumored that Amazon will start selling Kindle in Japan for some time, but this article refers not to Kindle, but just "SIM card". It says the plan is a prepaid plan with 1980 yen per month (approx. $23) for 500MB. Base service is provided by NTT DoCoMo, and Amazon is buying the capacity from its MVNO, Japan Communications (so Amazon will become a grandchild of DoCoMo, so to speak), and it can be used by any DoCoMo smartphone/tablets.
That means Kindle will most likely be DoCoMo-based, one way or another. Kindle is said to be coming out this summer in Japan.
Nikkei does not specify any source on this article (typical for their Sunday speculation article), so please take it as a grain of salt.